Waters are moved during annotation using the perceived space group's
symmetry operation. So if the authors give the wrong space group, then the
annotation pipeline understandably messes things up. If the originally
uploaded PDB file was kept by PDBe, then the problem can be recovered quite
easily by the annotators. Perhaps the topic starter, Michel Fodje, can send
a bug report to PDBe. In my experience, the annotators are very helpful
resolving these matters.
<potential flame>
Hoping that the depositors solve the problem by themselves, is probably in
vain: There are many crystallographers who do not read the CCP4BB (which is
a shame, really); they didn't notice the enormous amount of water related
bumps in their final model (which is in the validation report you get after
deposition and in REMARK 500 of the PDB file you have to approve); they also
didn't notice the huge number of symmetry-related bumps; the R-factors in
the PDB file are different from (and better than) the ones in Table 1. Also
notice that the paper was submitted on April 21st 2009 and the model was
deposited on June 29th 2009. Paper accepted on July 8th 2009. But I'm sure
the referees had a chance to properly assess the quality of the structure
model ;-)
</ potential flame>
Cheers,
Robbie
P.S. It's pretty awesome that the problem was solved in less than 20 minutes
by the CCP4BB (that is, by Phoebe Rice)
> -----Original Message-----
> From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
> Garib N Murshudov
> Sent: Friday, April 12, 2013 21:39
> To: [log in to unmask]
> Subject: Re: [ccp4bb] Puzzling Structure
>
> It is typo:
> R factor for p212121 - 0.4
> for p21212 - around 0.18
>
> Although water seem to have been moved around using p212121
>
>
>
>
> On 12 Apr 2013, at 16:33, Phoebe A. Rice wrote:
>
>
> Looks like a typo to me: if you change the CRYST space group record
> from P212121 to P21212, as the paper says it is, the packing problem goes
> away.
>
> ++++++++++++++++++++++++++++++++++++++++++
>
> Phoebe A. Rice
> Dept. of Biochemistry & Molecular Biology
> The University of Chicago
>
> 773 834 1723; [log in to unmask]
> http://bmb.bsd.uchicago.edu/Faculty_and_Research/
>
> http://www.rsc.org/shop/books/2008/9780854042722.asp
>
> ________________________________________
> From: CCP4 bulletin board [[log in to unmask]] on behalf of
> Michel Fodje [[log in to unmask]]
> Sent: Friday, April 12, 2013 2:17 PM
> To: [log in to unmask]
> Subject: Re: [ccp4bb] Puzzling Structure
>
> By the way, you will need to show symmetry atoms to see the
> problem.
>
>
>
> -----Original Message-----
>
>
> From: CCP4 bulletin board [mailto:[log in to unmask]]
> On Behalf Of
>
>
> Michel Fodje
>
>
> Sent: April-12-13 1:14 PM
>
>
> To: [log in to unmask]
>
>
> Subject: [ccp4bb] Puzzling Structure
>
>
>
> Has anyone else noticed a problem with the structure of the
> N-terminal
>
>
> capsid domain of HIV-2 PDB 2wlv.
>
>
>
> Load it up to in coot and navigate to residue B118.
>
>
>
>
>
> /Michel.
>
>
> Dr Garib N Murshudov
> Group Leader, MRC Laboratory of Molecular Biology Francis Crick Avenue
> Cambridge Biomedical Campus Cambridge
> CB2 0QH UK
> Email: [log in to unmask]
> Web http://www.mrc-lmb.cam.ac.uk <http://www.mrc-lmb.cam.ac.uk/>
>
>
>
>
>
>
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